Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 873, P. 162322 - 162322

Published: Feb. 18, 2023

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this only possible an in-depth overview of technological discussion pros cons available methods. We therefore conducted systematic literature review 407 peer-reviewed papers on aquatic published between 2012 2021. observed gradual increase in annual number publications from four (2012) 28 (2018), followed growth 124 This was mirrored tremendous diversification methods all aspects workflow. For example, freezing applied preserve filter samples, whereas we recorded 12 different preservation 2021 literature. Despite ongoing standardisation debate community, field seemingly moving fast opposite direction discuss reasons implications. Moreover, compiling largest PCR-primer database date, provide information 522 141 species-specific metabarcoding primers targeting wide range organisms. works as user-friendly 'distillation' primer that hitherto scattered across hundreds papers, list also reflects which taxa are commonly studied technology environments such fish amphibians, reveals groups corals, plankton algae under-studied. Efforts improve sampling extraction specificity reference databases crucial capture these ecologically important future surveys. In rapidly diversifying field, synthetises procedures can guide users towards best practice.

Language: Английский

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ITS alchemy: On the use of ITS as a DNA marker in fungal ecology

Fungal ecology, Journal Year: 2023, Volume and Issue: 65, P. 101274 - 101274

Published: July 26, 2023

High throughput sequencing of PCR amplicons derived from environmental DNA (aka metabarcoding) has become an integral part fungal ecology, enabling in-depth characterization communities. In most cases, the rDNA Internal Transcribed Spacer (ITS) region, which a long history as target in systematics, is used barcode marker. Despite improvements techniques and bioinformatics approaches, there are inherent limitations associated with use single-locus marker that often ignored. this text, I discuss both biological methodological ITS For example, proper species delimitation not possible single marker, significant barcoding gap (i.e. interspecific divergence) missing between sister taxa ITS. Further, we can rarely be fully confident about assigned species-level taxonomy based on available reference sequences. addition to limitations, extra layer complexity variation blended into metabarcoding data due errors may look similar natural molecular variation. The processing must take account basic properties well generated biases. regard, cannot adopt approaches settings other markers, such 16S 18S, blindly. intraspecific variability sometimes intragenomic variability, sequences clustered approach level resolution community studies. Therefore, argue concept amplicon sequence variants (ASVs) applicable. Although region by far best option general (meta)barcoding for fungi, contribution meant remind against naive or simplistic stimulating further discussions.

Language: Английский

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Future of DNA-based insect monitoring

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(7), P. 531 - 544

Published: March 10, 2023

Language: Английский

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Conceptual and empirical bridges between micro- and macroevolution

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(8), P. 1181 - 1193

Published: July 10, 2023

Language: Английский

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Environmental DNA: The next chapter

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 16, 2024

Abstract Molecular tools are an indispensable part of ecology and biodiversity sciences implemented across all biomes. About a decade ago, the use implementation environmental DNA (eDNA) to detect signals extracted from samples opened new avenues research. Initial eDNA research focused on understanding population dynamics target species. Its scope thereafter broadened, uncovering previously unrecorded via metabarcoding in both well‐studied understudied ecosystems taxonomic groups. The application rapidly became established research, field by its own. Here, we revisit key expectations made land‐mark special issue Ecology 2012 frame development six areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour environment (6) reference database development. We pinpoint success eDNA, yet also discuss shortfalls not met, highlighting areas priority identify unexpected developments. In parallel, our retrospective couples screening peer‐reviewed literature with survey users including academics, end‐users commercial providers, which address focus efforts advance eDNA. With rapid ever‐increasing pace technical advances, future looks bright, successful applications best practices must become more interdisciplinary reach full potential. Our retrospect gives towards concretely moving forward.

Language: Английский

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Extracting abundance information from DNA‐based data

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(1), P. 174 - 189

Published: Aug. 20, 2022

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference species interactions, modelling population dynamics distributions, biomonitoring environmental state change, false positives negatives. However, multiple sources bias noise in sampling processing combine inject error into sets. To understand how extract abundance information, it is useful distinguish two concepts. (i) Within-sample across-species quantification describes relative abundances one sample. (ii) Across-sample within-species each individual varies sample sample, such as over a time series, an gradient or different experimental treatments. First, we review literature on methods recover (by removing what call "species pipeline biases") "pipeline noise"). We argue that many ecological questions can be answered with just quantification, therefore demonstrate use "DNA spike-in" correct for information. also introduce model-based estimator used sets without physical spike-in approximate noise.

Language: Английский

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Novel community data in ecology-properties and prospects

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 39(3), P. 280 - 293

Published: Nov. 8, 2023

Language: Английский

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Optimizing insect metabarcoding using replicated mock communities

Methods in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 14(4), P. 1130 - 1146

Published: Feb. 13, 2023

1: Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies its performance not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms presence-absence, abundances, biomass. 2: Here we use mock experiments simple probabilistic model evaluate effect different DNA extraction protocols on performance. Specifically, ask four questions: (Q1) How consistent are recovered profiles across replicate communities?; (Q2) does choice lysis buffer affect recovery original community?; (Q3) estimates affected by differing times homogenization?; (Q4) Is possible obtain adequate abundance through biological spike-ins? 3: We show that quite variable replicates. general, mild protocol better at reconstructing lists approximate counts, while homogenization retrieving biomass composition. Small insects more likely be detected lysates, some tough require detected. Results less replicates lysates than homogenates. Some associated with strong PCR amplification bias, which complicates reconstruction counts. spike-in data, determined roughly 40% standard error homogenates, 50% under ideal conditions. latter case, however, this often requires species-specific reference data generalizes 4: conclude non-destructive, approach shows highest promise presence/absence description community, also allowing future morphological or molecular work material. However, perform composition, particular

Language: Английский

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Towards holistic insect monitoring: species discovery, description, identification and traits for all insects

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments the paucity of data on abundance, biomass traits. We here outline how these deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) specimens from mass samples obtained biomonitoring sites. barcodes are then used group into molecular operational units subsequently tested/validated as a second source (e.g. morphology). New described using barcodes, images short diagnoses, abundance collected both new specimen discovery become raw material training artificial intelligence identification algorithms collecting trait such body size, feeding modes. Additional can vouchers by genomic tools developed ecologists. Applying this pipeline few per site will lead greatly improved regardless whether composition sample is determined images, metabarcoding or megabarcoding. article part theme issue 'Towards toolkit global biodiversity monitoring'.

Language: Английский

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eDITH: An R‐package to spatially project eDNA‐based biodiversity across river networks with minimal prior information

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(5), P. 806 - 815

Published: March 27, 2024

Abstract Ecological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups the assessment ecological indices. Yet, most current approaches are not exploiting full potential eDNA largely interpreting results localized perspective. In riverine networks, by explicitly modelling hydrological transport associated decay, hydrology‐based models enable upscaling eDNA‐based diversity information, providing spatially integrated inference. To capitalize on these unprecedented data translate it into space‐filling projections, streamlined implementation needed. Here, we introduce eDITH R‐package, implementing model to project networks with minimal prior information. couples species distribution relating local taxon's shedding rate streamwater covariates, mass balance expressing concentration at river's cross‐section as weighted sum upstream contributions, an observational accounting for uncertainties measurements. By leveraging replicated measurements hydro‐morphological disentangling various sources, produces maps spatial any chosen resolution. applicable both metabarcoding taxon whose can be retrieved streamwater. The package provides user‐friendly functions single‐run execution fitting Bayesian methods (via BayesianTools package) non‐linear optimization. An interface DHARMa allows validation via posterior predictive checks. Necessary preliminary steps such watershed delineation characterization implemented rivnet package. We illustrate 's workflow functionalities two case studies from published fish data. eDITH, specifically intended ecologists conservation biologists. It used without previous knowledge but also customization experienced users. Ultimately, river globally, transforming how state change systems tracked high resolution highly versatile manner.

Language: Английский

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